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Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
Abstract
We demonstrate in this work that the surface tension, water‐organic solvent, transfer‐free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well‐known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25°C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.
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Items 101–136 of 136
Jepson, B. J. N., Mohan, S., Clarke, T. A., Gates, A. J., Cole, J. A., Butler, C. S., Butt, J. N., Hemmings, A. M., & Richardson, D. J. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m607353200 · Cited by 120
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Das, D., & Georgiadis, M. M. (2004) · Structure · doi:10.1016/j.str.2004.02.032 · Cited by 117
Stolt, P. C., Jeon, H., Song, H. K., Herz, J., Eck, M. J., & Blacklow, S. C. (2003) · Structure · doi:10.1016/s0969-2126(03)00068-6 · Cited by 117
Langlois d'Estaintot, B., Santambrogio, P., Granier, T., Gallois, B., Chevalier, J. M., Précigoux, G., Levi, S., & Arosio, P. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.04.036 · Cited by 113
Budayova‐Spano, M., Lacroix, M., Thielens, N. M., Arlaud, G. J., Fontecilla‐Camps, J. C., & Gaboriaud, C. (2002) · The EMBO Journal · doi:10.1093/emboj/21.3.231 · Cited by 111
The Frameshift Infidelity of Human DNA Polymerase λ
Bebenek, K., Garcia-Diaz, M., Blanco, L., & Kunkel, T. A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m305705200 · Cited by 104
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Guerrero-Valero, M., Ferrer-Orta, C., Querol-Audí, J., Marin-Vicente, C., Fita, I., Gómez-Fernández, J. C., Verdaguer, N., & Corbalán-García, S. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813099106 · Cited by 104
Structural basis for SH3 domain‐mediated high‐affinity binding between Mona/Gads and SLP‐76
Harkiolaki, M., Lewitzky, M., Gilbert, R. J. C., Jones, E., Bourette, R. P., Mouchiroud, G., Sondermann, H., Moarefi, I., & Feller, S. M. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg258 · Cited by 102
Structure of NFAT1 bound as a dimer to the HIV-1 LTR κB element
Giffin, M. J., Stroud, J. C., Bates, D. L., von Koenig, K. D., Hardin, J., & Chen, L. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb981 · Cited by 102
Hill, J. M., Vaidyanathan, H., Ramos, J. W., Ginsberg, M. H., & Werner, M. H. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf641 · Cited by 100
Rudenko, G., Bonten, E., d'Azzo, A., & GJ Hol, W. (1995) · Structure · doi:10.1016/s0969-2126(01)00260-x · Cited by 97
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Orth, P., Reichert, P., Wang, W., Prosise, W. W., Yarosh-Tomaine, T., Hammond, G., Ingram, R. N., Xiao, L., Mirza, U. A., Zou, J., et al. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.10.037 · Cited by 90
Bonten, E. J., Campos, Y., Zaitsev, V., Nourse, A., Waddell, B., Lewis, W., Taylor, G., & d'Azzo, A. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.031419 · Cited by 87
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Beard, W. A., & Wilson, S. H. (1998) · Chemistry & Biology · doi:10.1016/s1074-5521(98)90081-3 · Cited by 86
Kitahara, R., Yamada, H., Akasaka, K., & Wright, P. E. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00449-7 · Cited by 85
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Dementieva, I. S., Tereshko, V., McCrossan, Z. A., Solomaha, E., Araki, D., Xu, C., Grigorieff, N., & Goldstein, S. A. N. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.01.030 · Cited by 79
Boudsocq, F. (2002) · DNA Repair · doi:10.1016/s1568-7864(02)00019-8 · Cited by 79
Casal, E., Federici, L., Zhang, W., Fernandez-Recio, J., Priego, E.-M., Miguel, R. N., DuHadaway, J. B., Prendergast, G. C., Luisi, B. F., & Laue, E. D. (2006) · Biochemistry · doi:10.1021/bi060717k · Cited by 77
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Lai, L., Yokota, H., Hung, L.-W., Kim, R., & Kim, S.-H. (2000) · Structure · doi:10.1016/s0969-2126(00)00179-9 · Cited by 71
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Werner, M. H., Clore, G. M., Fisher, C. L., Fisher, R. J., Trinh, L., Shiloach, J., & Gronenborn, A. M. (1997) · Journal of Biomolecular NMR · doi:10.1023/a:1018399711996 · Cited by 68
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Mackereth, C. D., Schärpf, M., Gentile, L. N., MacIntosh, S. E., Slupsky, C. M., & McIntosh, L. P. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.094 · Cited by 67
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David, G., Blondeau, K., Schiltz, M., Penel, S., & Lewit-Bentley, A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m304484200 · Cited by 63
Wong, G. W., Yasuda, S., Madhusudhan, M. S., Li, L., Yang, Y., Krilis, S. A., Šali, A., & Stevens, R. L. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m108677200 · Cited by 61
Structural Basis for Phosphotyrosine Recognition by Suppressor of Cytokine Signaling-3
Bergamin, E., Wu, J., & Hubbard, S. R. (2006) · Structure · doi:10.1016/j.str.2006.06.011 · Cited by 60
Ravaud, S., Stjepanovic, G., Wild, K., & Sinning, I. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m710493200 · Cited by 59
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Shiba, T., Kametaka, S., Kawasaki, M., Shibata, M., Waguri, S., Uchiyama, Y., & Wakatsuki, S. (2004) · Traffic · doi:10.1111/j.1600-0854.2004.00188.x · Cited by 56
Crystal Structure of an Archaeal Actin Homolog
Roeben, A., Kofler, C., Nagy, I., Nickell, S., Ulrich Hartl, F., & Bracher, A. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.01.096 · Cited by 53
Kaneko, T., Kumasaka, T., Ganbe, T., Sato, T., Miyazawa, K., Kitamura, N., & Tanaka, N. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m306677200 · Cited by 51
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Zhao, F., Zhang, X., Liang, C., Wu, J., Bao, Q., & Qin, S. (2006) · Physiological Genomics · doi:10.1152/physiolgenomics.00255.2005 · Cited by 47
Protein complexes at the microtubule organizing center regulate bipolar spindle assembly
Rodriguez, A. S., Killilea, A. N., Batac, J., Filopei, J., Simeonov, D., Lin, I., & Paluh, J. L. (2008) · Cell Cycle · doi:10.4161/cc.7.9.5808 · Cited by 38
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Stroud, J. C., & Chen, L. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.09.065 · Cited by 35
Crystal structure of the MAP kinase binding domain and the catalytic domain of human MKP5
Tao, X., & Tong, L. (2007) · Protein Science · doi:10.1110/ps.062712807 · Cited by 31
Okamura-Ikeda, K., Hosaka, H., Yoshimura, M., Yamashita, E., Toma, S., Nakagawa, A., Fujiwara, K., Motokawa, Y., & Taniguchi, H. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.06.056 · Cited by 32
Ray, S. S., Bonanno, J. B., Chen, H., de Lencastre, H., Wu, S., Tomasz, A., & Burley, S. K. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10272 · Cited by 21
Zheng, Z., Dutton, P. L., & Gunner, M. R. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22779 · Cited by 13
Song, J., Gao, F., Cui, R. Z., Shuang, F., Liang, W., Huang, X., & Zhuang, W. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp304714q · Cited by 10
Metadata
- Authors
- Nicholls, A., Sharp, K. A., & Honig, B.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 1991-12
- Volume
- 11
- Issue
- 4
- Pages
- 281-296
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2106315897
- Cited by
- 5,240
- References
- 0
- FWCI
- 9.39
- Type
- journal article
- Language
- en
- Open access
- closed
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